Many SNPs that are predicted to encode deleterious amino acid variants. These mildly deleterious mutations may provide unique insights into population history, the dynamics of selection, and the genetic bases of phenotypes. This may be especially true for domesticated species, where a history of bottlenecks and selection can contribute to the accumulation of deleterious SNPs (dSNPs). Here we investigate the numbers and frequencies of deleterious variants in Asian rice (O. sativa), focusing on two varieties (japonica and indica) that may have been domesticated independently and their wild relative (O. rufipogon). Most dSNPs were lost during domestication, but comparative analyses in two population datasets indicated that the remaining dSNPs shifted in site frequency spectrum (SFS) relative to synonymous SNPs. Moreover, dSNPs were enriched within low recombination regions of the genome and experienced frequency increases similar to synonymous SNPs within regions of putative selective sweeps. A characteristic feature of rice domestication was a shift in mating system from outcrossing to predominantly selfing. Forward simulations suggest that this shift in mating system may have been the dominant factor in shaping extant rice diversity.